3) Preparing and running NGS_DNA pipeline

1) Copy rawdata to rawdata ngs folder

scp –r SEQSTARTDATE_SEQ_RUNTEST_FLOWCELLXX username@yourcluster:${root}/groups/$groupname/${tmpDir}/rawdata/ngs/

2) Create a folder in the generatedscripts folder

mkdir ${root}/groups/$groupname/${tmpDir}/generatedscripts/TestRun

3) Copy samplesheet to generatedscripts folder

scp –r TestRun.csv username@yourcluster:/groups/$groupname/${tmpDir}/generatedscripts/

Note: the name of the folder should be the same as samplesheet (.csv) file

4) Run the generate script

module load NGS_DNA
cd ${root}/groups/$groupname/${tmpDir}/generatedscripts/TestRun
cp $EBROOTNGS_DNA/generate_template.sh .
bash generate_template.sh
cd scripts

Note: If you want to run the pipeline locally, you should change the backend in the CreateInhouseProjects.sh script (this can be done almost at the end of the script where you have something like: sh ${EBROOTMOLGENISMINCOMPUTE}/molgenis_compute.sh search for –b slurm and change it into –b localhost

bash submit.sh

5) Submit jobs

Navigate to jobs folder. The location of the jobs folder will be outputted at the step before this one (step 4).

bash submit.sh

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